fix `shigatyper --version` inconsistency - update to __init__.py to 2.0.5

[kapsakcj]

Thanks for merging my last PR. It looks like __init__.py was not updated prior to the 2.0.4 release, and so shigatyper --version incorrectly reports v2.0.3

to reproduce:

# create mamba/conda env, pin v2.0.4
mamba create -n shigatyper204 -c conda-forge -c bioconda -c defaults shigatyper=2.0.4

# activate environment
mamba activate shigatyper204

$ shigatyper --version
ShigaTyper 2.0.3

# double-check it's using the correct executable
$ command -v shigatyper
/home/curtis_kapsak/miniconda3/envs/shigatyper204/bin/shigatyper

This PR should resolve the error by updating __init__.py with 2.0.5 in anticipation of the next patch release

We can see updated output that reports the updated version in the github actions logs

[kapsakcj]

GHActions log shows the expected 2.0.5 version ✅ :

usage: shigatyper.py [-h] [--R1 FASTA] [--R2 FASTA] [--SE FASTA] [--ont]
                     [-n SAMPLE_NAME] [-o OUTDIR] [--verbose] [--version]
ShigaTyper v. 2.0.5, 2022
A WGS-based genoserotyping pipeline for Shigella spp.
Yun Wu, Henry K Lau, Teresa Lee, David K Lau, Justin Payne
    The bacteria Shigella spp., consisting of 4 species and >50
serotypes, cause shigellosis, a foodborne disease of significant
morbidity, mortality, and economic loss worldwide. Classical Shigella
identification based on selective media and serology is tedious,
time-consuming, expensive, and not always accurate. Molecular diagnostic
assay does not distinguish Shigella at species level or from
enteroinvasive Escherichia coli (EIEC). We inspected the whole genome
sequencing (WGS) data from 21[9](https://github.com/CFSAN-Biostatistics/shigatyper/actions/runs/5281853880/jobs/9555985752?pr=16#step:6:10) Shigella isolates and observed low
concordance rate between conventional designation and molecular
serotyping, 86.8% and 78.9% at species and serotype level, respectively.
Serotype determinants for 6 additional serotypes were identified.
Examination of differentiation gene markers commonly perceived as
characteristic hallmarks in Shigella showed high variability among
different serotypes. Using this information, we developed ShigaTyper, an
automated workflow that utilizes limited computational resources to
accurately and rapidly determine 58 Shigella serotypes using Illumina
paired end WGS reads. Shigella serotype determinants and species-specific
diagnostic markers were first identified through read alignment to an
in-house curated reference sequence database. Relying on sequence hits
that passed a threshold level of coverage and accuracy, serotype can be
unambiguously predicted within 1 min for an average sized WGS sample of
~500 MB. Validation with WGS data from [11](https://github.com/CFSAN-Biostatistics/shigatyper/actions/runs/5281853880/jobs/9555985752?pr=16#step:6:12)2 isolates show an accuracy of
98.2%. This pipeline is the first step towards building a comprehensive
WGS-based analysis pipeline of Shigella spp. in a field laboratory
setting, where speed is essential and resources need to be more
cost-effectively dedicated.
optional arguments:
  -h, --help            show this help message and exit
  --R1 FASTA            Input FASTQ is R1 of paired-end reads
  --R2 FASTA            Input FASTQ is R2 of paired-end reads
  --SE FASTA            Input FASTQ is contains single-end reads
  --ont                 The input FASTQ file contains ONT reads
  -n SAMPLE_NAME, --name SAMPLE_NAME
  -o OUTDIR, --outdir OUTDIR
                        Where to write output files to
  --verbose, -v
  --version             show program's version number and exit
ShigaTyper 2.0.5

[kapsakcj]

@crashfrog @florathecat Is there anything else that needs to be completed prior to making another version release for shigatyper? Any other code changes to add to this PR?

I made this PR in anticipation of the next patch release. I was hoping it could get pushed to bioconda and that I could make another docker image for the next version. (which I assume will be v2.0.5, but let me know if you'd rather use a different number)

[florathecat]

Hi Curtis,

Not from my end at this moment. Thank you so much for all you have done for shigatyper.

Yun

From: Curtis Kapsak @.> Sent: Monday, July 3, 2023 2:27 PM To: CFSAN-Biostatistics/shigatyper @.> Cc: florathecat @.>; Mention @.> Subject: Re: [CFSAN-Biostatistics/shigatyper] fix shigatyper --version inconsistency - update to init.py to 2.0.5 (PR #16)

@crashfrog https://github.com/crashfrog @florathecat https://github.com/florathecat Is there anything else that needs to be completed prior to making another version release for shigatyper? Any other code changes to add to this PR?

I made this PR in anticipation of the next patch release. I was hoping it could get pushed to bioconda and that I could make another docker image for the next version. (which I assume will be v2.0.5, but let me know if you'd rather use a different number)

— Reply to this email directly, view it on GitHub https://github.com/CFSAN-Biostatistics/shigatyper/pull/16#issuecomment-1618980773 , or unsubscribe https://github.com/notifications/unsubscribe-auth/AB4KBBJO77KIOWYQKCOYRNLXOMFGNANCNFSM6AAAAAAZIFSFPE . You are receiving this because you were mentioned. https://github.com/notifications/beacon/AB4KBBL67KJWOCLJDE5JK2DXOMFGNA5CNFSM6AAAAAAZIFSFPGWGG33NNVSW45C7OR4XAZNMJFZXG5LFINXW23LFNZ2KUY3PNVWWK3TUL5UWJTTAP6X2K.gif Message ID: @. @.> >